Volume 19, Issue 8, Pages 1097-1107 (August 2011) The Structural Basis for the Function of Two Anti-VEGF Receptor 2 Antibodies  Matthew C. Franklin, Elizabeth C. Navarro, Yujie Wang, Sheetal Patel, Pinki Singh, Yi Zhang, Kris Persaud, Amtul Bari, Heather Griffith, Leyi Shen, Paul Balderes, Paul Kussie  Structure  Volume 19, Issue 8, Pages 1097-1107 (August 2011) DOI: 10.1016/j.str.2011.01.019 Copyright © 2011 Elsevier Ltd Terms and Conditions

Figure 1 Structures of KDR Domain 3 Bound to 1121B and 6.64 Fabs (A) Overview of the KDR:6.64 complex. A cartoon representation of the 6.64 Fab bound to domain 3 of KDR is shown with the Fab heavy chain in dark blue, the Fab light chain in light blue, and KDR domain 3 in magenta. The domain 3 N terminus is indicated at the upper right, and the C terminus is near the center of the image. (B) Overview of the KDR:1121B complex. A cartoon representation of the 1121B Fab bound to KDR domain 3 is shown aligned so that the KDR portion superimposes on the KDR portion of the complex in (A). As above, KDR domain 3 is in magenta, while the 1121B Fab heavy chain is in dark yellow and the light chain is in light yellow. This color coding will be maintained in all subsequent figures. (C) Electron density from the KDR:6.64 complex. A 2mFo − DFc map is shown as a blue mesh, contoured at 1 σ, in a region at the interface of KDR, the Fab heavy chain, and the Fab light chain. Selected residues from the three chains are labeled; LC indicates the Fab light chain, and HC indicates the Fab heavy chain. (D) A cartoon view of KDR domain 3. Secondary-structure elements have been labeled, and the N and C termini are labeled for comparison with other figures. (E) Electron density from the KDR:1121B complex, depicted as in (C). The Fab light chain is colored yellow, and is visible on the left side of the image. See also Figure S1. Structure 2011 19, 1097-1107DOI: (10.1016/j.str.2011.01.019) Copyright © 2011 Elsevier Ltd Terms and Conditions

Figure 2 Details of the KDR-Antibody Interfaces (A) Details of the KDR:6.64 interface. The molecular surface of KDR domain 3 is shown. Atoms which directly contact (<3.5 Å distance) an atom of the 6.64 Fab are colored red, while atoms which are close to the Fab (<5 Å distance) are colored pink. The six CDRs of the 6.64 Fab are shown as ribbons, colored as in Figure 1A. The large protrusion from the top center of the KDR surface in this view is one of the two N-glycosylations in the structure. The positions of the N and C termini of the KDR model are indicated. (B) A cartoon view of KDR domain 3, in exactly the same orientation as (A). If any atom of a particular residue was colored red in (A), the backbone is colored red here. If an atom was colored pink (but none were red), the backbone is pink here. Selected secondary-structure elements are labeled. (C) Details of the KDR:1121B interface. KDR domain 3 is depicted as in (A), but here shows interactions with the 1121B Fab. The CDRs of the Fab are shown, colored as in Figure 1C, except for CDR L2, which makes no contacts. (D) A cartoon view equivalent to (B), but for the KDR:1121B interface. The orientation of (C) and (D) is related to that of (A) and (B) by an approximate 90° rotation about a horizontal axis. (E) Details of the KDR d3:1121B interface. The backbones of KDR and 1121B are shown in cartoon representation, with KDR d3 colored pink, the 1121B light chain in yellow, and the 1121B heavy chain in brown. Side chains which form interactions between KDR and 1121B are shown in stick form. KDR residues are identified by residue number only, while 1121B heavy-chain residues have the prefix “H” and light-chain residues have the prefix “L.” See Figure S2 for another depiction of the KDR-1121B contacts. Structure 2011 19, 1097-1107DOI: (10.1016/j.str.2011.01.019) Copyright © 2011 Elsevier Ltd Terms and Conditions

Figure 3 A Schematic of the KDR Mutagenesis (A) The sequence of KDR domain 3 is shown, with the residues involved in mutants M1–M7 and M9 colored red. Residues contacting the 1121B light chain have a yellow dot above them, while residues contacting the 1121B heavy chain have a brown dot above them; if a residue contacts both chains of the Fab, it has both dots above it. Similarly, light blue and dark blue dots are used to indicate contacts to the 6.64 light and heavy chains, respectively. See Figure S2 for a detailed list of antibody-KDR contacts. (B) The top (domain 2-proximal) surface of KDR domain 3 is shown, with the N terminus indicated. Residues colored red were mutated to alanine; the surface patches corresponding to particular mutants are delineated by black lines. The two uncolored patches in the middle of the surface correspond to main-chain atoms of unmutated (hydrophobic core) residues. The bound 1121B Fab is shown in cartoon representation. (C) The surface of KDR domain 3 is shown in the same orientation as Figure 2A, with the 6.64 CDRs drawn as thin Cα traces for reference. The red surface corresponds to mutants M6 and M7, separated by the black line as indicated. See also Table S2 for KDR mutant expression levels. Structure 2011 19, 1097-1107DOI: (10.1016/j.str.2011.01.019) Copyright © 2011 Elsevier Ltd Terms and Conditions

Figure 4 KDR Mutant Binding ELISAs Binding curves to 1121B Fab (A), 6.64 Fab (B), and VEGF-165 (C) are shown for KDR d1–3 mutants M2–M7 and d1–3 wild-type. Points and error bars represent mean ± SEM of duplicate or triplicate measurements. Curves are nonlinear fits to a single-site binding equation. See Figure S3 and Table S1 for additional KDR mutant binding data. Structure 2011 19, 1097-1107DOI: (10.1016/j.str.2011.01.019) Copyright © 2011 Elsevier Ltd Terms and Conditions

Figure 5 KDR-Blocking ELISAs (A) 1121B Fab blocking the binding of KDR d1–3-Fc, d1–7-Fc, or d1–7-AP to VEGF-165. Points and error bars represent mean ± SEM of duplicate or triplicate measurements. Curves are nonlinear fits to a single-site inhibition equation, with fixed KD and concentration for the KDR-VEGF interaction as described in Experimental Procedures. (B) As in (A), but showing 6.64 Fab blocking. Structure 2011 19, 1097-1107DOI: (10.1016/j.str.2011.01.019) Copyright © 2011 Elsevier Ltd Terms and Conditions

Figure 6 Mechanism of Action of 1121B and 6.64 (A) Binding of 1121B, 6.64, and VEGF to KDR domain 3. The KDR:1121B and KDR:6.64 structures have been superimposed on their common KDR domain 3. KDR domain 3 from the KDR:6.64 complex is shown in surface representation, while the superimposed 1121B and 6.64 Fabs are shown in cartoon representation, colored as in Figure 1. The contact patches (corresponding to the pink and red coloring in Figure 2) are shown in brown for 1121B and blue for 6.64. Additionally, the contact patch of VEGF-C (Leppänen et al., 2010) is shown in green. (B) Steric clash between 1121B and VEGF. The KDR d2–d3:VEGF-C structure (Leppänen et al., 2010) is shown in cartoon representation, with KDR colored magenta and the two chains of VEGF-C colored black and white. The superimposed KDR:1121B structure is shown with the Fab in surface representation, colored as in Figure 1B. The red patch in the foreground on the surface of 1121B represents those atoms within 2.2 Å of an atom in VEGF-C. Additional red patches in the background indicate 1121B atoms within 2.2 Å of an atom in the superimposed KDR domain 2. (C) Noninterference of 6.64 with the KDR:VEGF dimer. The full dimer of KDR d2–d3 bound to VEGF-C (Leppänen et al., 2010) is shown in cartoon representation, colored as in (B), while two copies of the 6.64 Fab, colored as in Figure 1A, are superimposed on each copy of KDR domain 3. Structure 2011 19, 1097-1107DOI: (10.1016/j.str.2011.01.019) Copyright © 2011 Elsevier Ltd Terms and Conditions